Evaluation of β-Amino Acid Replacements in Protein Loops: Effects on Conformational Stability and Structure

Chembiochem. 2018 Mar 16;19(6):604-612. doi: 10.1002/cbic.201700580. Epub 2018 Feb 13.


β-Amino acids have a backbone that is expanded by one carbon atom relative to α-amino acids, and β residues have been investigated as subunits in protein-like molecules that adopt discrete and predictable conformations. Two classes of β residue have been widely explored in the context of generating α-helix-like conformations: β3 -amino acids, which are homologous to α-amino acids and bear a side chain on the backbone carbon adjacent to nitrogen, and residues constrained by a five-membered ring, such the one derived from trans-2-aminocyclopentanecarboxylic acid (ACPC). Substitution of α residues with their β3 homologues within an α-helix-forming sequence generally causes a decrease in conformational stability. Use of a ring-constrained β residue, however, can offset the destabilizing effect of α→β substitution. Here we extend the study of α→β substitutions, involving both β3 and ACPC residues, to short loops within a small tertiary motif. We start from previously reported variants of the Pin1 WW domain that contain a two-, three-, or four-residue β-hairpin loop, and we evaluate α→β replacements at each loop position for each variant. By referral to the ϕ,ψ angles of the native structure, one can choose a stereochemically appropriate ACPC residue. Use of such logically chosen ACPC residues enhances conformational stability in several cases. Crystal structures of three β-containing Pin1 WW domain variants show that a native-like tertiary structure is maintained in each case.

Keywords: Pin1 WW; alpha/beta-peptides; beta-hairpins; conformation analysis; foldamers; protein design.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acids / chemistry*
  • Cycloleucine / analogs & derivatives*
  • Cycloleucine / chemistry
  • Models, Molecular
  • Molecular Structure
  • Protein Stability
  • Proteins / chemistry*
  • Temperature


  • Amino Acids
  • Proteins
  • Cycloleucine
  • cispentacin